[Bioperl-l] phylip - ProtDist Problem

[Jason Stajich]

Well for starters what does this print?

print $protdist->executable


On Aug 31, 2004, at 10:04 PM, Nathan Haigh wrote:

> Yes, I have the ENV variable set to 3.6
>
> I first noticed it not working when using V3.6a3, and thought I'd 
> install
> the latest version 3.61 to see if this fixed the problem - but it 
> didn't.
>
> I checked what keystrokes were being piped into ProtDist, and the only 
> the
> menu choice was a 'Y' (which should just run the program, and hasn't
> changed between version). I ran the program manually and gave it the
> filename that had been used by ProtDist.pm and everything worked
> correctly!
>
> I've compared what has been sent to both SeqBoot and ProtDist (in 
> terms of
> menu choices etc) and they seem to have the same syntax etc. However, 
> as
> I've said ProtDist doesn't seem to want to get past the line:
>
> 	open(PROTDIST,"|".$self->executable);
>
> Any ideas, why this particular line is causing the problems? Could it 
> be
> something to do with BioPerl or maybe my OS? If you have any thoughts 
> on
> debugging this, I'd like to know!
>
> Thanks
> Nathan
>
>> -----Original Message-----
>> From: Jason Stajich [mailto:jason at cgt.duhs.duke.edu]
>> Sent: 31 August 2004 12:48
>> To: nathanhaigh at ukonline.co.uk
>> Cc: bioperl
>> Subject: Re: [Bioperl-l] phylip - ProtDist Problem
>>
>> Hmm - there are some changes in PHYLIP 3.6 from 3.5 menus, did you 
>> make
>> sure your PHYLIP version environment was set by setting the ENV
>> variable otherwise the wrong commands are sent in.
>>
>> PHYLIPVERSION=3.6
>>
>> Also you are using 3.6.1 which I know has some bug fixes over 3.6 but
>> may also have incurred some changes in how the menus act - I don't
>> really know though.
>>
>> I guess either use 3.5 or try debugging the running of 3.6.1 by 
>> putting
>> some print statements in there - see what is being sent in to protdist
>> and then run protdist by hand to see what are the expected menu items
>> to get what you want.  That is how Shawn and I built this in the first
>> place.
>>
>> -jason
>> On Aug 31, 2004, at 9:26 PM, Nathan Haigh wrote:
>>
>>> I am trying to run the following script at the bottom which takes a
>>> SimpleAlign object and runs SeqBoot on it. I would then like to take
>>> this
>>> output and run ProtDist, Neighbor and Consense to produce a bootstrap
>>> consensus tree. However, ProtDist just seems to fail when it gets to
>>> this
>>> line in ProtDist.pm:
>>>
>>> 	open(PROTDIST,"|".$self->executable);		# line 399 in the
>>> latest version of ProtDist.pm from the CVS
>>>
>>> I am running this on WinXP from within a cgi script and have phylip
>>> v3.61. I
>>> have no idea why this should fail as the similar line in SeqBoot 
>>> works
>>> fine!
>>>
>>> Has anyone come across this problem or know why this might be
>>> happening!?
>>>
>>> Regards
>>> Nathan
>>>
>>>
>>>
>>> # use seqboot to generate bootstrap alignments
>>> my @params_seqboot = ('datatype'=>'SEQUENCE', 'replicates'=>100);
>>> my $seqboot_factory =
>>> Bio::Tools::Run::Phylo::Phylip::SeqBoot->new(@params_seqboot);
>>> my $aln_ref = $seqboot_factory->run($aln);
>>>
>>> # create distance matrices and construct trees using neighbor
>>> my $protdist_factory =
> Bio::Tools::Run::Phylo::Phylip::ProtDist->new();
>>> my $neighbor_factory =
> Bio::Tools::Run::Phylo::Phylip::Neighbor->new();
>>> my @tree;
>>> foreach my $a (@{$aln_ref}) {
>>> 	my $matrix = $protdist_factory->run($a);
>>> 	push @tree, $neighbor_factory->run($matrix);
>>> }
>>> # use consense to get a final tree
>>> my $consense_factory =
> Bio::Tools::Run::Phylo::Phylip::Consense->new();
>>> my $tree = $consense_factory->run(\@tree);
>>>
>>> # output treefile
>>> my $outfilename = "outtrees_ur/homologene.nh"; # unrooted tree
>>> my $outtree = new Bio::TreeIO('-format' => 'newick',
>>> 				'-file'   => ">$outfilename");
>>> $outtree->write_tree($tree);
>>>
>>>
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>>>
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>>>
>> --
>> Jason Stajich
>> Duke University
>> jason at cgt.mc.duke.edu
>
>
--
Jason Stajich
Duke University
jason at cgt.mc.duke.edu